Maniac
Apolyton Sage
Instead of having Transcendence happen automatically after building a huge project, have the player actually take part--In order for transcendence to work, the player must guide the fungus growth so that it can expand enormously (as it does in the end movie of Alpha Centauri), but still not destroy all human life anyway. Transcendence is terribly dangerous, and it is only through skilled guidance that Planet does not kill everyone off. "Tending" the fungus growth could range from manually planting fungus, to taking your own improvements and city buildings offline so as to lessen your impact on Planet. This would obviously make you much more vulnerable to attack, but could be balanced somewhat by the fact that Planet would be busy trying to kill everyone else. You could also "help" Planet by waging war against the terraforming states. This way Transcendence can be a bit more involved and interesting--you have to actually play your way through this ending.
That's more or less the idea with the current victory when the Flowering Counter crosses 100.
I think that there should be something more to the "white pine council member==>win" scenario. Perhaps you should have to be the "leader" of the council (assuming it is run like the UN).
Otherwise, if you are a very minor player, or are on the verge of losing, you shouldn't "win" just by choosing Hybrid Ecology at the last moment.
Regarding preventing a switch on the last moment, I was thinking once the Flowering Counter has passed a certain number, you could no longer switch to the Hybrid ecology civic, and the sides for the 'final battle' would be set.
Regarding only the leader council winning. My fear kinda is, that to become the leader, you might have to kill off or weaken your best friends. Personally I kinda like the idea of large 'alliance' victories, as long as, to spice up the endgame, there will be another alliance actively trying to prevent you from winning.